The problem is you have a group of cells connected on a busbar, so any readings you're getting at the cell won't be accurate. There is some voltage drop present or otherwise all the readings would be the same volts.
As to why you saw the initial cell voltage on some cells at 2.6V and some at 3.3V is because you didn't top balance them in parallel. The higher voltage cells will bleed off to the lower voltage cells once the busbar connected all the cells. The Batrium probably had nothing to do with it.
Take this photo for instance. I see a group of 4 cells with the + on one end all connected to the busbar. That puts the cells in parallel. The cells will balance with each other, no different than top balancing in parallel.
As for the nut welding on the stud, as long as current is passing thru the threads, you will find arcing. If you have ever used an arc welder and used the outside of a nut to connect the negative cable, you will find the current passing thru the threads has welded the nut solid to the stud or bolt. The reason is the arcing that occurs, threads are not perfect mating surfaces and thus there is resistance and arcing. Two things occur, mini arcs just like the arc welder and excessive heating of the threads on both surfaces leading to distortion.
Have you loaded the cells down and test capacity? Results will probably be all over the place as the voltage drop/resistance across the terminals won't be even.